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- PDB-8pqt: Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis therm... -

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Basic information

Entry
Database: PDB / ID: 8pqt
TitleNucleoside 2'deoxyribosyltransferase from Chroococcidiopsis thermalis PCC 7203 WT bound to Bis-Tris
ComponentsNucleoside 2-deoxyribosyltransferase
KeywordsTRANSFERASE / Bis-Tris / WT
Function / homologydeoxyribonucleoside monophosphate catabolic process / 5-hydroxymethyl-dUMP N-hydrolase activity / : / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase / transferase activity / metal ion binding / Nucleoside 2-deoxyribosyltransferase
Function and homology information
Biological speciesChroococcidiopsis thermalis PCC 7203 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTang, P. / Harding, C.J. / Czekster, C.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other privateSBS0-YGS014 United Kingdom
CitationJournal: Acs Catalysis / Year: 2024
Title: Snapshots of the Reaction Coordinate of a Thermophilic 2'-Deoxyribonucleoside/ribonucleoside Transferase.
Authors: Tang, P. / Harding, C.J. / Dickson, A.L. / da Silva, R.G. / Harrison, D.J. / Czekster, C.M.
History
DepositionJul 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside 2-deoxyribosyltransferase
B: Nucleoside 2-deoxyribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7974
Polymers35,3782
Non-polymers4182
Water5,332296
1
A: Nucleoside 2-deoxyribosyltransferase
B: Nucleoside 2-deoxyribosyltransferase
hetero molecules

A: Nucleoside 2-deoxyribosyltransferase
B: Nucleoside 2-deoxyribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5948
Polymers70,7574
Non-polymers8374
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_556x,x-y,-z+4/31
Buried area13160 Å2
ΔGint-46 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.189, 131.189, 86.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-403-

HOH

21B-361-

HOH

31B-367-

HOH

41B-435-

HOH

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Components

#1: Protein Nucleoside 2-deoxyribosyltransferase


Mass: 17689.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chroococcidiopsis thermalis PCC 7203 (bacteria)
Strain: PCC 7203 / Gene: Chro_1188 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: K9TVX3
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 9.8 mg/ml enzyme; 22.5% v/v PEG Smear Broad; 0.1 M Bis-Tris pH 7.5; 0.05 M Zinc acetate dihydrate; 0.2 M Lithium sulfate

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→113.61 Å / Num. obs: 48818 / % possible obs: 100 % / Redundancy: 50.9 % / CC1/2: 1 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.02 / Rrim(I) all: 0.146 / Net I/σ(I): 19.6
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 29.5 % / Rmerge(I) obs: 1.626 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2409 / CC1/2: 0.955 / Rpim(I) all: 0.299 / Rrim(I) all: 1.654 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
PHENIX1.19.2-4158phasing
xia23.3.4data reduction
xia23.3.4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→69.04 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2251 2485 5.1 %
Rwork0.1905 --
obs0.1923 48768 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→69.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2413 0 28 299 2740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0422561
X-RAY DIFFRACTIONf_angle_d1.7083474
X-RAY DIFFRACTIONf_dihedral_angle_d16.273385
X-RAY DIFFRACTIONf_chiral_restr0.062364
X-RAY DIFFRACTIONf_plane_restr0.011447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.32161480.30122508X-RAY DIFFRACTION100
1.73-1.770.26611350.25072533X-RAY DIFFRACTION100
1.77-1.810.26851120.23852553X-RAY DIFFRACTION100
1.81-1.850.27061240.22422551X-RAY DIFFRACTION100
1.85-1.90.25891390.21152527X-RAY DIFFRACTION100
1.9-1.950.28281220.21392555X-RAY DIFFRACTION100
1.95-20.26491370.21322508X-RAY DIFFRACTION100
2-2.070.25841530.19832540X-RAY DIFFRACTION100
2.07-2.140.26381360.18482538X-RAY DIFFRACTION100
2.14-2.230.2251220.17422578X-RAY DIFFRACTION100
2.23-2.330.19481400.16482528X-RAY DIFFRACTION100
2.33-2.450.21321540.16492559X-RAY DIFFRACTION100
2.45-2.610.22761290.18042570X-RAY DIFFRACTION100
2.61-2.810.24651340.17522598X-RAY DIFFRACTION100
2.81-3.090.23531390.17582584X-RAY DIFFRACTION100
3.09-3.540.20841380.1722623X-RAY DIFFRACTION100
3.54-4.460.15881570.14982637X-RAY DIFFRACTION100
4.46-69.040.23171660.23522793X-RAY DIFFRACTION100

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